[gmx-users] pdb file of polymer

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 29 20:27:08 CEST 2012

On 6/29/12 2:21 PM, Parvez khan wrote:
> Hi, I am trying to do polymer simulation with gromacs. I am new to
> gromacs and trying to construct topology for a system of polymer
> chains. My problem is that i am facing difficulties to creat pdb file
> for polymer chain containing 1000 monomers. I have used PRODRG server
> but it gives me a pdb and topology file up to maximum 41 monomers
> chain. I am not understanding what wrong with PRODRG server. Is there

Nothing is wrong.  It's just that PRODRG limits how many atoms are allowed in 
the input structure.

> any server or tool for generating db file.

There are lots of ways to generate a coordinate file.  Here are some suggestions:




Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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